Python NewickPhyloImporter Examples

Example #1

File: default.py Project: pombredanne/django-phylogeny

class PhyloImporterTestCase(TestCase):
	'''Tests phylogeny importers.'''
	
	def setUp(self):
		# exporter
		self.phyloxml_importer = PhyloXMLPhyloImporter()
		self.nexus_importer = NexusPhyloImporter()
		self.newick_importer = NewickPhyloImporter()
		# expected phyloxml
		phyloxml_path = ''
		phylogeny_path = phylogeny.__path__
		for path in phylogeny_path:
			phyloxml_path = os.path.join(phyloxml_path, path)
		self.phyloxml_path = os.path.join(phyloxml_path, 'tests', 'expected-phyloxml.xml')
		# expected nexus
		nexus_path = ''
		phylogeny_path = phylogeny.__path__
		for path in phylogeny_path:
			nexus_path = os.path.join(nexus_path, path)
		self.nexus_path = os.path.join(nexus_path, 'tests', 'expected-nexus.nex')
		# expected newick
		newick_path = ''
		phylogeny_path = phylogeny.__path__
		for path in phylogeny_path:
			newick_path = os.path.join(newick_path, path)
		self.newick_path = os.path.join(newick_path, 'tests', 'expected-newick.tree')
	
	def testPhyloXMLImport(self):
		self.phyloxml_importer.import_from = self.phyloxml_path
		self.phyloxml_importer.save()
		self.assertEqual(Taxon.objects.count(), 13)
	
	def testNexusImport(self):
		self.nexus_importer.import_from = self.nexus_path
		self.nexus_importer.save()
		self.assertEqual(Taxon.objects.count(), 13)
	
	def testNewickImport(self):
		self.newick_importer.import_from = self.newick_path
		self.newick_importer.save()
		self.assertEqual(Taxon.objects.count(), 13)

Example #2

File: default.py Project: pombredanne/django-phylogeny

	def setUp(self):
		# exporter
		self.phyloxml_importer = PhyloXMLPhyloImporter()
		self.nexus_importer = NexusPhyloImporter()
		self.newick_importer = NewickPhyloImporter()
		# expected phyloxml
		phyloxml_path = ''
		phylogeny_path = phylogeny.__path__
		for path in phylogeny_path:
			phyloxml_path = os.path.join(phyloxml_path, path)
		self.phyloxml_path = os.path.join(phyloxml_path, 'tests', 'expected-phyloxml.xml')
		# expected nexus
		nexus_path = ''
		phylogeny_path = phylogeny.__path__
		for path in phylogeny_path:
			nexus_path = os.path.join(nexus_path, path)
		self.nexus_path = os.path.join(nexus_path, 'tests', 'expected-nexus.nex')
		# expected newick
		newick_path = ''
		phylogeny_path = phylogeny.__path__
		for path in phylogeny_path:
			newick_path = os.path.join(newick_path, path)
		self.newick_path = os.path.join(newick_path, 'tests', 'expected-newick.tree')